Hi,
I came to US on 1 Oct 2011 on H1b.My spouse and kid are on H4.

For 2011 I filled a 1040 as married filling jointly along with W-7 for my kid.After doing so I realized I should have filled a 1040 NR.While doing so I did not attach a statement about making First Year choice which is jointly signed by me and my spouse indicating that we are doing First Year Choice.

I realized my mistake and filed a 1040X with a 1040NR (Amended) 1 week after that.

Because there are different deductions available in 1040 and 1040 NR,my refund got reduced.Now I am worried that if IRS processes the first return and sends me money how do I return the difference back to IRS?

Pub 519 states that in case the taxpayer does not indicate First year choice by a joint declaration signed by both spouses,it won't be considered as one.

You over-reacted.

You could have sent in the First Year choice statement after the fact to keep your joint return valid.

However, it is LIKELY the IRS will NOT accept the amended return because, once you file JOINTLY, it is a IRREVOCABLE decision.

The 1040 X Instructions Page 4 states clearly the following:

Resident and nonresident aliens. Use Form 1040X to amend Form 1040NR or Form 1040NR-EZ. Also, use Form
1040X if you should have filed Form 1040, 1040A, or 1040EZ
instead of Form 1040NR or 1040NR-EZ, or vice versa.
http://www.irs.gov/pub/irs-pdf/i1040x.pdf

Please let me know your thoughts.

That is technically true.

However, one of the foundation rules for the IRS is that a JOINT return can NEVER be changed to a Married Filing Separate return if the amendment is submitted AFTER the 17 April 2012 filing deadline. That is what you are attempting to do, and I am confident that the IRS WILL reject the amendment.

This works in your favor. When you get the rejection notice, you then need only send in the SIGNED Residency Choice Statement to meet all of the requirements.

Hi
In my case the last date is Oct 15,2012,since I filled a request for extension to file.
http://www.irs.gov/pub/irs-pdf/p501.pdf
Page 7 of this Publication States that One cannot amend from joint return to separate return after due date of return.Since in my case its Oct 15,2012,technically I am not past due date.

Did you report worldwide income for the entire year on the joint return?

Yes

The 17 April 2012 date for the restriction of amending from JOINT to Married Filing Separately CANNOT be extended.

Hence, it is my belief that the IRS WILL reject your amendment. If not, submit a second amendment to file jointly, because that IS the best way for you to file.